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2019-04-03Fixed an issue that caused global phenotype search to often not work and cert...zsloan
2019-04-03Fixed issue where strains could be added twice in the SNP browser, causing so...zsloan
2019-04-02Fixed issue where non-GEMMA mapping would throw an error because it would sti...zsloan
2019-03-29Fixed issue that caused PCA results to be different in GN2 than in GN1; one r...zsloan
2019-03-29Updated UCSC Verify link-out from hg19 to hg38 for humanszsloan
2019-03-28Added link to GN2 document github wiki to index pagezsloan
2019-03-28Possibly fixed issue where PCA traits didn't calculate for certain sets of tr...zsloan
2019-03-27Changed gen_select_dataset.py to be able to show multiple datasets under the ......Fixed issue where full description was given for some unpublished traits Fixed code related to editing certain pages (like news) with CKEditor, but it still won't work until the CKEditor library is included in GUIX or something zsloan
2019-03-25- Added SVG export to basic stats figures...- Fixed issues where some stats figures (mainly box and violin plots) didn't update correctly when sample values were changes - Fixed issue with some temp traits if user wasn't logged in - Fixed issue where traits couldn't be added to a collection from the correlation results page zsloan
2019-03-19Added option to add PCA traits to collection from correlation matrix pagezsloan
2019-03-18- Added PCA traits to correlation matrix. You can't change their names yet or......but you can click them and access them from the trait page. I'll add the option to access them from the corr matrix page as well, but adding the option to change their names might be trickier since they're currently used as their Redis keys. I need some better way of passing the Redis key around so it can be stored in collections, but this is tricky without changing the structure in ElasticSearch - Fixed the way temp traits work so you can use them with various functions, like mapping, correlations, network graph, etc - Fixed some appearance issue where the network graph options were too wide if a trait name was too long zsloan
2019-03-13Zooming into chromosome or remapping with GEMMA is now very fast, since it st......Added option to search for terms in quotes, searching for all the contents within the quotes Added link to R/qtl documentation when user is in the R/qtl mapping tab zsloan
2019-03-11Changed header style, because the jumbotrons previously used didn't look that...zsloan
2019-03-11Added default empty collection when user is logged in and attempts to add tra......Fixed issue with displaying cofactor selection tables for scatterplot Removed limit on text length for collection trait fields (dataset name and description) zsloan
2019-03-07Changed the way covariates are displayed when selected for mapping...Made the outlier notification appear for all mapping methods Removed some misleading text saying "Block samples" from the Transform and Filter Data section zsloan
2019-03-07Made violin plots for different groups/sample-sets different colors and match...zsloan
2019-03-07Fixed issue where pressing enter in the search page text area would go to a n......Also removed some pointless wrapper from dataset_select_menu_orig.js that was left over from being converted from coffeescript (need to do this with other files also) zsloan
2019-03-07Fixed issue where correlation results containing NaN results sorted incorrectly...Set default permutations for R/qtl to 200 zsloan
2019-03-06Cofactor option for correlation scatterplot was broken; it should be fixed now...Added title to basic stats table and made link for Interquartile Range more obvious Removed pointless "Delete Collection" button from correlation results page zsloan
2019-03-05Made R/qtl metho/model names better and added some javascript to disable wron...zsloan
2019-03-04Fixed excel export to show all columns...Fixed stats table to calculate Range and Interquartile Range correctly, and only show Range (fold) for appropriate traits zsloan
2019-03-04- Added z-score transformation...- Added text indicating which transformation has been applied zsloan
2019-03-01Added alternating point colors for manhattan plotszsloan
2019-03-01Changed loading page to work for any feature, instead of having to make a sep......Fixed some wrong text on heatmap page zsloan
2019-03-01Added more information to the top-right corner of the mapping results...Fixed sorting issues on correlation page zsloan
2019-02-27Added loading page for correlation...Added a better error page for mapping if no results are returned (which generally implied an error occurred during the running of GEMMA) Fixed some issues with tables, like them sorting incorrectly or showing the wrong number of digits zsloan
2019-02-22Fixed some appearance issues with several tables...Fixed issue where cofactor selection screens were broken Changed case attributes to be applied across groups, though need to discuss this with Rob since it shouldn't always be done this way Added new inversion transformation zsloan
2019-02-18Merge pull request #356 from pjotrp/gn-testing...Updated instructions and SERVER_PORT for single flask serverzsloan
2019-02-18typoPjotr Prins
2019-02-18Note on running testsPjotr Prins
2019-02-18Updated installation instructions and SERVER_PORT for single flask serverPjotr Prins
2019-02-18RELEASE-NOTESPjotr Prins
2019-02-15Fixed error caused by change to N values in database (now takes strings inste......Fixed error that caused N to show up as "null" in the trait sample table instead of "x" zsloan
2019-02-14Fixed minor bug with updating stats figures when sample values changedzsloan
2019-02-14Changed trait page tables to load JSON...Also fixed such that sorting works with user-updated values zsloan
2019-02-14Merge pull request #351 from pjotrp/gn-testing...Gn testing: updates to scripts, removed coffee scripts and removed pylmm codezsloan
2019-02-13Removed pylmm references and related functionsPjotr Prins
2019-02-13Removed listPjotr Prins
2019-02-13Remove all coffee filesPjotr Prins
2019-02-13Merge branch 'testing' of github.com:genenetwork/genenetwork2 into gn-testingPjotr Prins
2019-02-12Added GeneWeaver linkout...Fixed some issues with sorting in various tables Changed header appearance for some pages Fixed bug where basic stats table would sometimes be duplicated or show up with empty fields zsloan
2019-02-05Removed redundant header text from search page to save vertical spacezsloan
2019-02-05Fixed issue with getting marker info that affected heatmap and possibly other......Added the collection page features (correlation matrix, network graph, third party link-outs, etc) to the search result and correlation result pages zsloan
2019-02-04Changed the way the table is drawn for the search pages so that it can show w......Added typeahead to snp_browser (still need to tell it only to use it for rat, though) Added WebGestalt link to collection page (still need to add it and BNW to other trait list pages) zsloan
2019-01-22Fixed issue where Haplotype Analyst in mapping results would always show resu......Fixed issue where traits couldn't be added to a collection from the global search results Made some improvements to the gene global search table zsloan
2019-01-17Redid gene global search to take JSON data input instead of converting an HTM......Made some changes to make trait page SNPs link point to GN2 SNP Browser, as well as make other links open in new tabs/windows zsloan
2019-01-16Pushing SNP browser updateszsloan
2019-01-11Got InDel working for Variant Browser...Changed Variant Browser to display gene name under "Domain" when the user searches a gene term and rows are mislabeled "Intergenic" Fixed Chr option to display correct chromosomes for different species Fixed order for correlation drop-down on trait page Fixed some appearance issues with the mapping results table Improved appearance of correlation scatterplot page zsloan
2018-12-21Fixed collections so they can be very large (1000+ traits)...Added option to submit traits in collection to BNW Fixed issue with "x" values for user-submitted traits Fixed issue where post-publications descriptions were wrongly appearing in global search results zsloan
2018-12-05Fixed Verify linkzsloan
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